After another four solid seasons, Nerlinger moved to hometown club Borussia Dortmund, where he began suffering with injuries; this situation would be worsened in the following years, as he could hardly get a game at any of his following two clubs, Scotland's Rangers and 1. FC Kaiserslautern (he reunited with former Bayern teammate Carsten Jancker in the latter), forcing to his retirement from the game in December 2005.